Frank Gore’s nine-yard touchdown run in the fourth quarter gave the 49ers their first lead and ended up being the difference in San Francisco’s 28-24 comeback victory over Atlanta in the NFC championship game.

David Goldman/Associated Press

Frank Gore’s nine-yard touchdown run in the fourth quarter gave the 49ers their first lead and ended up being the difference in San Francisco’s 28-24 comeback victory over Atlanta in the NFC championship game.

ATLANTA – Make way Joe Montana and Steve Young. Colin Kaepernick is leading a brash new group of 49ers to the Super Bowl.

Frank Gore scored a pair of second-half touchdowns, and San Francisco, after falling behind 17-0 by the first play of the second quarter, pulled off a record rally for a 28-24 victory over the Atlanta Falcons in the NFC championship game Sunday.

Kaepernick didn’t put up the same dazzling numbers he did in the divisional playoff against Green Bay. But he was solid enough to justify coach Jim Harbaugh’s decision to bench Alex Smith and go with the youngster. The 49ers’ defense did its part, shutting out Atlanta in the second half and making a big stop with just over a minute to go.

San Francisco (13-4-1) moves on to face r Baltimore at New Orleans in two weeks and will try to join Pittsburgh as the only franchises with six Super Bowl titles. It could be a brother-vs.-brother matchup, too, since John Harbaugh coaches the Ravens.

“This is what we play for. We play for this moment,” said 49ers tight end Vernon Davis, who hauled in a touchdown pass from Kaepernick. “We put in all the hard work and get the opportunity to play on the big stage.”

Montana led the 49ers to four Super Bowl wins, and Young took them to No. 5. It’s up to Kaepernick to get No. 6 when the 49ers play in the NFL title game for the first time since 1995.

This also was sweet redemption after a bitter loss at home in last year’s NFC title game, when a fumbled return set up the New York Giants’ winning field goal in overtime.

“We’ve come full circle,” said Denise DeBartolo York, part of the family that has owned the 49ers since their championship days, “and the dynasty will prevail.”

The second-year quarterback who runs like a track star guided San Francisco on a pair of second-half scoring drives that wiped out Atlanta’s 24-14 lead at the break. Gore scored on a 5-yard run early in the third quarter, then sprinted in from 9 yards out for the winning score with 8:23 remaining after each team made crucial mistakes to ruin potential scoring drives.

On both of Gore’s touchdowns, the Falcons had to worry about Kaepernick running it himself out of the spread option, and they barely even touched the running back on either play. His backup, LaMichael James, also ran for a score in similar fashion.

“I kind of figured that coming in, and they showed that on film, so I assumed Frank and LaMichael were going to have a big day,” Kaepernick said. “Frank ran hard (Sunday), and I can’t say enough about him.”

The 49ers pulled off the biggest comeback victory in an NFC championship game, according to STATS. The previous NFC record was 13 points – Atlanta’s victory over Minnesota in the 1999 title game, which sent the Falcons to what remains the only Super Bowl in franchise history.

In the AFC, the record is 18 points, when Indianapolis rallied past New England in 2007.

The top-seeded Falcons (14-4), in what appeared to be the final game for Hall of Famer-to-be Tony Gonzalez, tried to pull off another season-extending drive. But, unlike the week before against Seattle, they needed a touchdown this time.

They came up 10 yards short.

On fourth down, Matt Ryan attempted a pass over the middle to Roddy White that would have been enough to keep the drive going. But linebacker NaVorro Bowman stuck a hand in to knock it away with 1:13 remaining.

The 49ers ran off all but the final 6 seconds, not nearly enough time for Ryan to pull off his greatest comeback yet.

With that, the celebration was on in the city by the bay, which rapidly is becoming the new Titletown USA. The 49ers will try to follow the lead of the baseball Giants, who won the World Series in October.

The Falcons came up short of their second Super Bowl, leaving the 1995 Braves as the city’s only major sports champions. This one figures to hurt for a while.

“We didn’t make the plays when we had the opportunity,” Falcons coach Mike Smith said. “There were five or six plays, like in most hard-fought games, that make a difference. There were ebbs and flows and changes in momentum, and they made more plays than we did.”

Kaepernick, who ran for 181 yards against the Packers to set an NFL playoff record for a quarterback, didn’t have much chance to use his legs against the Falcons. He broke off a 23-yard gain but was thrown for a 2-yard loss the only other time he carried the ball.

But Kaepernick showed he’s more than a runner, shredding the Falcons for 233 yards passing on a 16-for-21 day. His favorite receiver was Davis, who hauled in five passes for 106 yards, including a 4-yard touchdown.

Gore carried 21 times for 90 yards, while James added 34 yards on five carries.

Ryan finished 30 of 42 for 396 yards, by far the best performance of his playoff career. But his postseason record dropped to 1-4, done in by two big miscues – an interception and a fumble – in the second half.

Julio Jones was Ryan’s favorite receiver most of the day, finishing with 11 catches for 182 yards and a pair of touchdowns. He hauled in a 46-yarder less than 4 minutes into the game, then made a dazzling grab in the left corner of the end zone for a 20-yard score. He got his left foot down, then planted his right foot about an inch inside the line while cornerback Tarell Brown was all over him.

Ryan threw a 10-yard touchdown pass to Gonzalez with 25 seconds remaining in the first half after the 49ers had cut the deficit to 17-14. It seemed the home team had reclaimed the momentum heading to the locker room, but, amazingly, that would be its final score of the day. The 49ers quickly seized control on the opening possession of the second half, driving 82 yards in just seven plays for Gore’s first touchdown.

After a nearly perfect first half, in which Ryan was 18 of 24 for 271 yards and those three touchdowns, the quarterback known as Matty Ice made a couple of crucial blunders.

First, he tossed a pass that was picked off by Chris Culliver, halting a drive in 49ers territory. Ryan ripped off his chinstrap in disgust.

Then, with the Falcons in scoring range for at least a field goal, Ryan failed to grab a shotgun snap, appearing to take his eyes off the ball before he caught it. The ball squirted away and Aldon Smith recovered for the 49ers at their own 37.

“Against a good team, you can’t have those kind of mistakes,” Ryan said.

San Francisco also squandered some chances. Struggling kicker David Akers clanked a 38-yard field goal try off the upright, and Michael Crabtree fumbled just short of the goal line, the ball stripped away by Dunta Robinson and recovered by Stephen Nicholas. But, after that big defensive stop with 13½ minutes remaining, the Falcons went three-and-out.

The 49ers drove for the winning touchdown.

Atlanta drove 70 yards and might have reclaimed the lead if Harry Douglas had been able to stay on his feet while hauling in a 22-yard pass. The defender slipped and so did Douglas, but he managed to make the catch even though Harbaugh thought it touched the turf. The coach challenged the call and began hopping around in disbelief when the officials let it stand.

But he got his chance to celebrate at the end.

Gonzalez, who said all year he was 95 percent sure this would be his final season, sounded like he was done.

“I’ve had such a great life,” he said. “I wish it would’ve culminated with the Super Bowl, but it didn’t.”

At least Gonzalez finally won a playoff game. It took 16 years to get his first – the 30-28 victory over the Seahawks – but he couldn’t make it two wins in two weeks.

“If anybody out there is saying I’m going to have regrets, I’m telling you right now that’s not true,” the 36-year-old Gonzalez said.